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In bacterial two-component signaling involving the interaction of sensor kinases (SK) and response regulators (RR), the problem is partially solved since we observe that more than half of the SK/RRs are located adjacently on the chromosomes, and chromosomal adjacency is known to strongly imply interaction (e.g., [9]).
First, genes encoding successive steps of a biosynthetic pathway tend to be located adjacently on the chromosome in biosynthetic gene clusters (BGCs).
Both genes are located adjacently on chromosome 13 in a head to head orientation [9], [10], [16], [17].
Furthermore, we propose that two of the peptide genes were duplicated concomitantly with opioid receptor genes located adjacently in the same chromosomal regions.
For instance, four of small nuclear RNA/RNP complexes (snRNA/P) are located adjacently and form a clade (terminal leaves 39-400).
The presence of scpI and tnpA in between the satA and pgmA genes in the S. iniae chromosome also supports horizontal transfer theories since the homologues of satA and pgmA in GAS are located adjacently in the genome [39].
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This approach is based on an elegant idea presented in [18] utilizing an auxiliary pilot located at adjacently to the pilot and which cancels the interference of (21).
This scheme combines the action of a general and specific TF following a hierarchical logic mostly linked to catabolite repression: when glucose is absent, CRP regulation (X in most of these FFLs, Fig. 3.A) activates a number of genes enabling the sensing (Ys in FFLs, usually autoregulated) and metabolizing (Zs, adjacently or not adjacently located) of alternative sugar sources.
This unit was defined as the group of genes constituted by the operon encoding the TF acting as Y and, when applicable, by those of its Z-operons adjacently located (which included also second adjacents, to control for tandem duplications).
For the identification of genomic regions with enriched subnetworks of interacting genes we defined gene sets of genes that were adjacently located within a chromosomal region (co-located) from overlaping sliding windows along the human chromosomes.
The maximum synteny score ( = 2) was assigned to those ORFs fully syntenic as they were located between two adjacently conserved genes, while ORFs with only one adjacent gene was conserved were given a lower score ( = 1).
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